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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa04LNT0287600.2

GCGCTTCGATTATTGCAGTTTTTTTTGGTTGAAAGCATGTAGAGGAATCTCAATACACATAAATCCTGATACAATATCAACTAAGTTTAATGTCTAGGAAGACTCGATGAAACATGAAAACAGTGGACTGCCGTGCGAGTTACAAATCATCTAGGATAAGAGTTAAACCGATACTGATTCCTAAGTGGAACCTACAAAATATCAGGTTTCGTGGTTCCGGTGGCCTGCACCGAATAGGTAACAGAGAGTTCTGGAAACATGTACGGCGTACATGCAAGATACAAATTTGGGACTTCTGACGACGTGCATTGTCGAGAGCAAGAGTGCCACCATGCACTGCAGAATCCTCCTGGAAGCCCAGAAATGGCACCATGTTCTCTCACTTCAGGACAGATACCGTGGATCATTTCCTTGCTTTCCCATCTTATGCACATCCTCAGGTGAAAGTATCTTGATGTACCATACACTATTCACAAAGGACCTACATCATATGAGGAAGGTCAGTTTCAAGAAGAATCATGTCTGATGTTTACTCTCACGAAGGGTCTTGGGTAACTGAGCATCAACATATAGTGACTGACCAACACATATTATTGAAGGAAGAACAGTCTAGTAAAAAAATTTAACATATTAATACACATTAAAGATGTATGACTGAATGCACATGAATTCTGTTTGAGATCACAATTAGGCACCGAACATTGCAAAAATATACTCCATATAACACTAGTACTTTTAAACATATTCATTAGATACTGTCCATGAGCTGTCAACATGTCTTTCAGTGAATGAAGAAGGGATATCCATTCACATTGTACATACCTTTCCTCGATAAGCTATTAGTTGTGGAAACCAGGAAACCAAAGTATTGTACTCCCTCCGTTTCATAATGTAAGACTTTTTAGCATTGCTCACATTCATATAGATGTTAATGAATCTAGACACACATATATTTCTAGATTCATTAACATCTATATGAATGTGGGCAATGCTAGAAAGTCTTACATTATGAAACGGAGGAAGTATAAGACAGCCACTTTTGCACTTGCTAGTCAAGCCAAATTTTGTTGATCTTAGGCACGTTTAATATCTTTAAATTATTTAGATATACAATGAAGTTACAATGCCTGATGTAGATTTGAAATTTTTACTTAGCATGTTAACTTGGCCGTTTTGAGGCCAACATCAATTAAGAGATTCAGTTTGTAGTGTGCACACATGGACAGGGTATGCCAAGTGTAGTACTAAAATTTAAGCAGATTTTTTTGCAACCAAATCATAGAACGGTAAGATGAAACTTAAATTTATATTGCTTACTAAAACTTGAATTTGTAGTGCGCATGCATGGATATTGATTACTAAAACTAATAAATAAATCAGAATTCTGAGAATATTTCTTACTCCCAAGGGTCGTCTCCAAGGAGAAGCACATCATTCTCCCTGTCGACGAATACAAGCTGCCAGCCTGATCTATCAGGGTCGTCCAATTGACCCTTAATGCCGAACATCTGACCCAGTTCTTCTCGAAGTTCAGCATAATTAGAGAACCGGGTTATGTCCAACGACCTCCCAACCGAACCTGACTTGTAAACCTTCACAAATGTTCTGGTTGCTGGATCGTTCTCTCCTGTATTTTGCAATAAACCAGAAGAGTCGTCCAAGCAACCATACATTGCATTCTGCAGATAAGTTGATCCAGAAGGGATCGTTGATAAGTTGCCATCCGAAACATTCGAAGTCAGATTAGGAACCATGTTGTACAGGAGGGATGAAGAGTCAACTTGTGGACTAAAAAGGGACTGGTTTTGCACATCACGACCAATTTTGTTTTCAACAGAACCATCTTTGCTTGTGGGTGAGTTATGCAAAACCGAGCCCCCAAAAGACACTGACTGTGAACCCATAAACTTCTGCTTCCATGCCTGTTGCTGCTGCTGCTGCTGCTCACTAGCTACAGGCTGATTAAATCGAGATAAGTCCACAGCTTTCGAACTTCCCTGAAGGAAGCTCGAATCCAACATGTTATCACTACTGCTAGAGGTGATGAAGCTTGAAGAATTCGCATTAGGATCAGAGAAGCCAAATTTTTCTCGCAAATGACTCGGTAATGATGTTGGACTTGGGAGAACTGCACTTGTAGGAACTTGGTAGCTTTGATCTGGTTGAATCTTCTGCTTCTGATCATTCTGAACTTGCTGCATTTGCTGTAGTTGCTGGAGTTGCTGTTGTATAGCACTTGGGCTCAACATCGTTTGGATATTTTGGGCATCAGGATTAATTATCTGTTGCTGGCTTGCTTGCTGCAGAATTTGTTGCTGCAATAATGGGTTGAGGTTGCAGTGTTCTTGAGGGGACTGCATAGGTTGCTGAAGGTGCAAGAATTGCTGTTTTAAGTAACCACCAGATTGGGAAGCAGCAGCAGCAGCAACTACTGCTTGGTACTGATCGTGATCGCTGCTCAGTAAGGATGGATGGAGCCTCTGTTGTCCCCAGGAGCCAATACCAGGTGACTGAAAGTTCAGAGACTGAAAACCTCCCTCACCAGCAACTCCTCTCAGCCACATTAAAGCATTGCTGTCATCTTAAGTGTGATACAGCAGTTAATAAAAGAACAGAAATATGAATGAGAGATACTAGAAAATGGAATTATGTCAGGCAGATCAATGCATTCTCCATAACAAGAATGCACAGAAAGACAATGAATAAAAAGAATGCATATTATAGAACGTTACATTTGCTACGGAAGAGCCTTATCAAATAACATTGATCCACCTTGGGTGCTTAAGAAATGGAAGGAAGAGATCAACTTTTCACTTACACCATAACTTGTTTTACTTTTAGCCTATATGAGCATTTTATAAAGTTCCCTGATCAATCTCTGTATCCAGAACCATCATTTGAGGCATATTGTTCACAGTAGAGAACACTGACTTGAACTATAGCCTCTTGCTCTTGCACCACAATCTCAACTTCAGGTTATTTTAGTTAGAATCATCAGCTGGTTGATGTGGCAGGTTCAGAAATTTATTAAGGCTGTGGCTTCAGTAATTTGAGTGTGATGGCTAAAACACTATGTAAATGCACCAAATAAACTTCCACATGATAGGCGCACACACATAGCAAGCATACAGCAAAATAGCTTCAAAACTAGTTTATGCCTGACACACAGTAACAAGAATCTTAAGCGTACCATGCAGGGAAGCAACTCCTGAATACCAAGGATGCTTAACTCTCAGTGGGAACAGAGATGGATACATTGGAAAGGTTGTCAATGGTTCAATTTCCCATAAAGAAACTCTTGGTGGTCTTTCCCCTGCAGTTGATTCATCCCAACCAACCTTCACAGATCTCCAATAGGAACTAGGCCAACGGACTGGGTCTGCATCACTAACTTCAGTTATAGTCCCCATATACCTGCGAACGCTTGATTCCTCAGTCTCAAACAACATCCTGAACCGCATCCCAACCGATATCCGGGTGTGAAAAACAGCCTTGATGTATTTTGACAGTGGTATGACAAATTCTGATGGACTTGCCCGGGGGTTGTAGAAAATAGTGAAACGGCTGTTTGTAGCAGCAGCATGAGCTGCTGCTGCAAGGAGACCTATGTGCATGCTATCGCTTGAAAGAACAGAGGAAGGCATCACAGTCTGTGGCCGACTGGCACGTCTTATTCCAAGTAAAAGCTGGTTTTTCTCGTTCCATATGAAAAGCACAGAATCTCCAGCAACAAGTCTCTTAGCACTGACAAAAACGCTCCAGCCAGTGGTTAGCAGGTGTCGTTTGGGTTGGCCTCGAAAGATGTGCCTGAACTTCCACTCGATGTCATGAATATCCCGTGCAATTAGCTCCTGGGCTGGAGGCTGCTGTGTGAAATCCTACAAACCACACTATACCACCTGTTATTGGCAACAGCAAAACCCAACCACCCAAGAAGTACAAGAAAGGAGCACAGCCCCAAATTACACCACTCATCACACCAAAGGAGGGAAGACGCGCTCAGCAGCACGGCGGGGCACGGAGAACCCCCCGTGCGTGCTGGTGTCGCTCGCCGTCAATGTCTTGCAGAAGTAATTCGTCGGCTGCTTGCTCATTATCCCCATCTCCGCGGGAAGGTACGCATCGTTCTGCTCTGGGTTCAGTGGCTGGAGCGTCATCTGCGCGTACACCTCGTCAGTCTCCACATCCGCATGCATTGTGACATCGTGGAGCTGGCAGATCAGCTGCGCCGGCAGGTTGGGGTAGTTCGGGATGTGACCCTCCACCTCCTTGTTCGTCGACGCCGCCACCTGCTCGCTGTGGCCTTGCGGGAAGTAGACGACGCGCGTGCCGACGGTGGGGAGGCAGACGAGCGGGCCGGCGCAGGCGTGCCATAGCTCCGAGTTGAGGCACTTCTTCTCTAGCCACCCACCTTCCTCGGGCGGCGCGGGGGGCGGCGGCGGCTGCGGCGGCCCGATGCTGGCCGCCGACGACGAGCTCATCTCCTCCTCCTCCGACCAAACCAGAGAAGCACAAACTCTTAATCTATCCCCTCACAAATCCACCCGAAAACCCCATCCCCCTCCTCAAATCGGCCGCATTCTTTCTCTTCCGCTCACCCGAGCTCGGAGATCGCCACCATGGTGGGGAGAAAGGGTGGGGTTGGAGAGAGAGAGAGAGAGCGCAAGAGGGGTGGAAATGATTAGGTTTGTGGCATTTAAGCGAGAGAGAGAGAGAGAGAGAAAGAGAGGGGTTCGCGTGGTTCGAGTAGTGCGAGTGCGTGTGTGCGTGTGCGCGACGAGGGGGGGCGCAGCGCAGGGGGCCGTACAGTAGCG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.42208
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0287600.2 4 34279062 G C
Osa04LNT0287600.2 4 34279654 G A
Osa04LNT0287600.2 4 34280646 C T
Osa04LNT0287600.2 4 34282799 A G
Osa04LNT0287600.2 4 34284562 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0287600.2 osa-miR5526 Cleavage 4.0 14.136 1 21
Osa04LNT0287600.2 osa-miR5820 Cleavage 4.5 10.697 1 21
Osa04LNT0287600.2 osa-miR5834 Translation 4.5 18.8 1 21
Osa04LNT0287600.2 osa-miR2873c Cleavage 4.0 22.909 1 21
Osa04LNT0287600.2 osa-miR529b Cleavage 4.0 15.845 1 21
Osa04LNT0287600.2 osa-miR1436 Cleavage 1.0 12.529 1 21
Osa04LNT0287600.2 osa-miR1439 Cleavage 3.0 12.709 1 21
Osa04LNT0287600.2 osa-miR1856 Translation 4.5 15.042 1 21
Osa04LNT0287600.2 osa-miR2090 Cleavage 5.0 14.584 1 22
Osa04LNT0287600.2 osa-miR2097-5p Translation 5.0 14.42 1 22
Osa04LNT0287600.2 osa-miR2118h Translation 5.0 9.498 1 22
Osa04LNT0287600.2 osa-miR2118i Translation 4.0 9.498 1 22
Osa04LNT0287600.2 osa-miR2118k Translation 5.0 9.498 1 22
Osa04LNT0287600.2 osa-miR3979-5p Translation 2.5 6.788 1 20
Osa04LNT0287600.2 osa-miR3979-5p Translation 4.5 22.869 1 20
Osa04LNT0287600.2 osa-miR5161 Translation 5.0 12.713 1 20
Osa04LNT0287600.2 osa-miR5496 Cleavage 5.0 17.082 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0287600.2 4 nan Resistance or Tolerance Drought tolerance RG143 RG620
Osa04LNT0287600.2 4 rpf4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0287600.2 4 gpps4.1 Resistance or Tolerance Drought tolerance RG214 RG620
Osa04LNT0287600.2 4 nan Morphological trait Panicle/flower RG620 RG214
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
Osa04LNT0287600.2 osa-MIR11336 92.208 154 1 154 1.85e-57 219
Osa04LNT0287600.2 osa-MIR11339 88.961 154 1 154 4.04e-49 191
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus